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- PDB-1i6u: RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROT... -

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Basic information

Entry
Database: PDB / ID: 1i6u
TitleRNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S8/RRNA COMPLEX FROM METHANOCOCCUS JANNASCHII
Components
  • 16S RRNA FRAGMENT
  • 30S RIBOSOMAL PROTEIN S8P
KeywordsRIBOSOME / protein-RNA interactions / ribosomal protein S8 / RNA
Function / homology
Function and homology information


cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #30 / Dna Ligase; domain 1 - #10 / Ribosomal Protein S8; Chain: A, domain 1 / Dna Ligase; domain 1 / : / Ribosomal protein S8 signature. / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Small ribosomal subunit protein uS8
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsTishchenko, S. / Nikulin, A. / Fomenkova, N. / Nevskaya, N. / Nikonov, O. / Dumas, P. / Moine, H. / Ehresmann, B. / Ehresmann, C. / Piendl, W. ...Tishchenko, S. / Nikulin, A. / Fomenkova, N. / Nevskaya, N. / Nikonov, O. / Dumas, P. / Moine, H. / Ehresmann, B. / Ehresmann, C. / Piendl, W. / Lamzin, V. / Garber, M. / Nikonov, S.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii.
Authors: Tishchenko, S. / Nikulin, A. / Fomenkova, N. / Nevskaya, N. / Nikonov, O. / Dumas, P. / Moine, H. / Ehresmann, B. / Ehresmann, C. / Piendl, W. / Lamzin, V. / Garber, M. / Nikonov, S.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site.
Authors: Nevskaya, N. / Tishchenko, S. / Nikulin, A. / al-Karadaghi, S. / Liljas, A. / Ehresmann, B. / Ehresmann, C. / Garber, M. / Nikonov, S.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA
Authors: Kalurachci, K. / Nikonowicz, E.P.
History
DepositionMar 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 16S RRNA FRAGMENT
D: 16S RRNA FRAGMENT
A: 30S RIBOSOMAL PROTEIN S8P
B: 30S RIBOSOMAL PROTEIN S8P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6618
Polymers53,2764
Non-polymers3844
Water3,873215
1
C: 16S RRNA FRAGMENT
A: 30S RIBOSOMAL PROTEIN S8P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7343
Polymers26,6382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 16S RRNA FRAGMENT
B: 30S RIBOSOMAL PROTEIN S8P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9265
Polymers26,6382
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.687, 121.687, 137.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain 16S RRNA FRAGMENT


Mass: 11894.089 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The rRNA fragment was obtained by transcription from synthetic DNA template using T7 RNA polymerase.
#2: Protein 30S RIBOSOMAL PROTEIN S8P


Mass: 14744.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJAS8 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P54041
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulphate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulphate11
2sodium cacodylate11
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlRNA1drop
23.5 mg/mlprotein1drop
32.8 Mammonium sulfate1drop
4100 mMsodium cacodylate1drop
52.2 Mammonium sulfate1reservoir
6100 mMsodium cacodylate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
31101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.97624,0.97933,0.97948
SYNCHROTRONESRF BM30A20.97949,0.97921,0.97435
SYNCHROTRONEMBL/DESY, HAMBURG X1130.91
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMay 17, 2000
MARRESEARCH2IMAGE PLATEJun 20, 2000
MARRESEARCH3CCDJun 25, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)MADMx-ray1
3Double crystal focussing monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.976241
20.979331
30.979481
40.979491
50.979211
60.974351
70.911
ReflectionResolution: 2.57→41.07 Å / Num. all: 30271 / Num. obs: 30271 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 64.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.249 / % possible all: 82.5
Reflection
*PLUS

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→41.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1361993.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1415 4.8 %RANDOM
Rwork0.218 ---
obs0.218 29179 89.9 %-
all-29396 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.43 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.77 Å20 Å20 Å2
2--3.77 Å20 Å2
3----7.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 1580 20 215 3843
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it1.532
X-RAY DIFFRACTIONc_scangle_it2.362.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 236 5.3 %
Rwork0.343 4253 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.21
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.379 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.343

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